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Zhou S, Feng X, Bai J, Sun D, Yao B, Wang K. Synergistic effects and competitive relationships between DOC and DOX as acting on DNA molecules: Studied with confocal Raman spectroscopy and molecular docking technology. Heliyon 2024; 10:e30233. [PMID: 38707315 PMCID: PMC11066432 DOI: 10.1016/j.heliyon.2024.e30233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
Docetaxel (DOC) is one of the second-generation antineoplastic drugs of the taxanes family with excellent antitumor activity. However, the mechanism of DOC inducing tumor cell apoptosis and treating cancer diseases, especially its interaction with DNA in the nucleus, and its adjuvant or combined Doxorubicin (DOX) acting on DNA molecules are unclear. In this study, the interaction mechanism between DOC and DNA, as well as the synergistic effects and competitive relationships among DOC and DOX when they simultaneously interact with DNA molecules were studied by laser confocal Raman spectroscopy combined with UV-visible absorption spectroscopy and molecular docking technology. The spectroscopic results showed that the binding constant of DOC to DNA is 5.25 × 103 M-1, the binding modes of DOC and DNA are non-classical intercalation and electrostatic binding, and the DNA-DOC complex has good stability. When DOC or DOX interacts with DNA alone, both of them can bind with bases and phosphate backbone of DNA, and also lead to DNA conformation changes; when DOC and DOX interact with DNA at the same time, the orders of interaction not only affect their binding sites with DNA, but also cause changes in the surrounding environment of the binding sites. In addition, the molecular docking results further verified that DOC and DOX have synergy and competition when they interact with DNA molecules simultaneously. The docking energies of DNA-DOC and DNA-DOX indicate the important role of van der Waals forces and hydrogen bonds. This study has practical significance for the design and development of antitumor drugs with less toxic based on the taxanes family and the combination with other drugs for the treatment of cancer.
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Affiliation(s)
- Suli Zhou
- Key Laboratory of Photoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China
| | - Xiaoqiang Feng
- Key Laboratory of Photoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China
| | - Jintao Bai
- Key Laboratory of Photoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China
| | - Dan Sun
- Key Laboratory of Photoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China
| | - Baoli Yao
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Kaige Wang
- Key Laboratory of Photoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an, 710127, China
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Gao X, Meng Q, Fang J, Shan S, Lin D, Wang D. Effects of particle size and pyrolytic temperature of biochar on the transformation behavior of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162923. [PMID: 36933735 DOI: 10.1016/j.scitotenv.2023.162923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Rampant use of antibiotics has caused a rapid dissemination of antibiotic resistance genes (ARGs) in environment, posing great threats to ecosystems and human health. Applying biochar (BC) in natural systems to combat the spread of ARGs arises as an attention-grabbing solution. Unfortunately, the effectiveness of BC is still unmanageable due to the incomprehensive knowledge over correlations between BC properties and extracellular ARGs transformation. To pinpoint the crucial factors, we primarily explored transformation behaviors of plasmid-mediated ARGs exposed to BC (in suspensions or extraction solutions), adsorption capacities of ARGs on BC, and growth inhibition of E. coli imposed by BC. Specifically, the effects of BC properties including particle size (large-particulate 150 μm and colloidal 0.45-2 μm) and pyrolytic temperature (300, 400, 500, 600, and 700 °C) on the ARGs transformation were emphasized. Results showed that both large-particulate BC and colloidal BC, irrespective of their pyrolytic temperature, would induce significant inhibitory effects on the ARGs transformation, while the BC extraction solutions showed little effect except BC pyrolyzed at 300 °C. Correlation analysis uncovered that the inhibition effect of BC on ARGs transformation was tightly correlated with its adsorption capacity towards plasmid. Accordingly, greater inhibitory effects from those BCs with higher pyrolytic temperatures and smaller particle sizes mainly originated from their greater adsorption capacities. Intriguingly, E. coli was unable to ingest the plasmid adsorbed on BC, which led to ARGs blocked outside the cell membrane, although this inhibitory effect was partially affected by survival inhibition of BC on E. coli. Particularly, significant plasmid aggregation could occur in the extraction solution of large-particulate BC pyrolyzed at 300 °C, leading to a significant inhibition of ARGs transformation. Overall, our findings complete the insufficient understanding over the effects of BC on ARGs transformation behavior, and potentially provide new insights to scientific communities in mitigating ARGs spreading.
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Affiliation(s)
- Xuan Gao
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, Hangzhou 310023, China; School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Qingkang Meng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jing Fang
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, Hangzhou 310023, China; School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China.
| | - Shengdao Shan
- Zhejiang Province Key Laboratory of Recycling and Ecological Treatment of Waste Biomass, Hangzhou 310023, China; School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Dengjun Wang
- School of Fisheries, Aquaculture and Aquatic Science, Auburn University, Auburn, AL 36849, USA
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Erkmen C, Unal DN, Kurbanoglu S, Eren G, Uslu B. Evaluation of the Interaction of Cinacalcet with Calf Thymus dsDNA: Use of Electrochemical, Spectrofluorimetric, and Molecular Docking Methods. BIOSENSORS 2022; 12:bios12050278. [PMID: 35624577 PMCID: PMC9138790 DOI: 10.3390/bios12050278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022]
Abstract
The binding of drugs to DNA plays a critical role in new drug discovery and is important for designing better drugs. In this study, the interaction and binding mode of calf-thymus double-stranded deoxyribonucleic acid (ct-dsDNA) with cinacalcet (CIN) from the calcimimetic drug that mimics the action of calcium on tissues group were investigated. The interaction of CIN with ct-dsDNA was observed by the differential pulse voltammetry (DPV) technique by following the decrease in electrochemical oxidation signals to deoxyguanosine and adenosine. A competitive study was performed on an indicator, methylene blue, to investigate the interaction of the drug with ct-dsDNA by fluorescence spectroscopy. Interaction studies have shown that the binding mode for the interaction of CIN with ct-dsDNA could be groove-binding. According to the results obtained, the binding constant values were found to be 6.30 × 104 M−1 and 3.16 × 105 M−1, respectively, at 25 °C as obtained from the cyclic voltammetry (CV) and spectroscopic techniques. Possible molecular interactions of CIN with dsDNA were explored via molecular docking experiments. The docked structure indicated that CIN could fit well into the minor groove of the DNA through H-bonding and π-π stacking contact with CIN.
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Affiliation(s)
- Cem Erkmen
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- The Graduate School of Health Sciences, Ankara University, Ankara 06110, Turkey
| | - Didem Nur Unal
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- The Graduate School of Health Sciences, Ankara University, Ankara 06110, Turkey
| | - Sevinc Kurbanoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
| | - Gokcen Eren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, Ankara 06330, Turkey;
| | - Bengi Uslu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- Correspondence:
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Tibbits G, Mohamed A, Call DR, Beyenal H. Rapid differentiation of antibiotic-susceptible and -resistant bacteria through mediated extracellular electron transfer. Biosens Bioelectron 2022; 197:113754. [PMID: 34773749 DOI: 10.1016/j.bios.2021.113754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 11/02/2022]
Abstract
Conventional methods for testing antibiotic susceptibility rely on bacterial growth on agar plates (diffusion assays) or in liquid culture (microdilution assays). These time-consuming assays use population growth as a proxy for cellular respiration. Herein we propose to use mediated extracellular electron transfer as a rapid and direct method to classify antibiotic-susceptible and -resistant bacteria. We tested antibiotics with diverse mechanisms of action (ciprofloxacin, imipenem, oxacillin, or tobramycin) with four important nosocomial pathogens (Acinetobacter baumannii, Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae) by adding the bacterial culture to a custom-designed electrochemical cell with a glassy-carbon electrode and growth media supplemented with a soluble electron transfer mediator, phenazine methosulfate (PMS). During cell respiration, liberated electrons reduce PMS, which is then oxidized on the electrode surface, and current is recorded. Using this novel approach, we were able to consistently classify strains as antibiotic-resistant or -susceptible in <90 min for methodology development and <150 min for blinded tests.
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Affiliation(s)
- Gretchen Tibbits
- The Gene and Linda Voil and School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Abdelrhman Mohamed
- The Gene and Linda Voil and School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Haluk Beyenal
- The Gene and Linda Voil and School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
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Ipte PR, Manna S, Sahoo S, Satpati AK. Probing the interaction of anti-HIV drug Darunavir with dsDNA and HSA using electrochemical and spectroscopic measurements. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 56:1435-1444. [PMID: 34986753 DOI: 10.1080/10934529.2021.2008205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 06/14/2023]
Abstract
Investigation of electrochemical and spectroscopic characteristics of anti-human immunodeficiency virus (HIV) drug provides important information related to the efficacy of the drug in relation with its interaction with several important biomolecules. In the present investigation we have developed an electrochemical and spectroscopic method for the detection of anti-HIV drug Darunavir (DRV) using the carbon paste as the working electrode. The analytical method has generated the detection limit of 1.86 µM (S/N = 3). The electrochemical investigations have also been carried out for the exploration of the interaction of DRV with double stranded deoxyribose nucleic acid DNA (dsDNA) and human serum albumin (HSA). Electrochemical investigations were supported from the spectroscopic measurements in evaluating the interaction. The results obtained from voltammetric and spectroscopic experiments shows strong interaction between the drug and the macromolecules. It has been observed that DRV forms strong complexes with HSA and dsDNA with the formation constants of 2.7 × 104 and 4.2 × 104 M-1 respectively. The formation constants are varied with the pH of the solution, which leads to the assertion of the mechanism of the interaction between DRV and dsDNA.
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Affiliation(s)
- Priyanka R Ipte
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sudipa Manna
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Srikant Sahoo
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashis Kumar Satpati
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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